Thanks for the replies Skater and P610. And what an unexpected surprise, P610, that you were the one who put that little info on the wiki. What happened for me was that I was running around town doing my stuff while also trying to get the homies achievement (although I do not know if CID counts, but I had Kinzie with me so meh why not have CID-and Keith David-tag along as well) and I used the abduction gun thinking that the homies are at a safe distance, but CID was very close to me 'cuz he's fast like that I guess
. I got a message about CID going away or something and then I figured he would become greyed out for a while (used with it from the past SR games), but at a certain point I couldn't call him back. I didn't tie this fact with the abduction gun however; but I checked the wiki and your valuable info saved me of some frustration on trying to figure out what the hell happened
I haven't yet received the "A game of clones" mission but when I will, I will return with info on whether CID has returned or not.
Update 1: still haven't gotten to the A game of clones mission, but I did have CID in a cutscene when entering The Broken Shillelagh to rescue Shaundi so I thought I might have gotten him/her/it back, but didn't
As I am writing this I come to a fearful realization that the A game of clones mission might get broken because of this CID bug; I've seen around the web people complaining that they couldn't start loyalty missions and such because homies were unavailable... oh boy
Update 2 (8th of January 2016): I just finished "A game of clones" mission and CID is still greyed out in the homies phone menu. Too bad, though I am thankful that this bug does not break the walkthrough. After I finish the game 100% maybe I will install a homies mod or something and bring him back
I will make a third update with the results if and when I do that.